One major problem faced by designers and users of mass spectrometers is the presence of chemical noise in the mass spectra. The source and appearance of chemical noise will vary according to the analyte type, ionization method, and operating conditions. For mass spectrometers utilizing matrix-assisted laser desorption/ionization (MALDI), most of the chemical noise is represented by groups of peaks corresponding to matrix cluster ions with compositions described by (Matrixx−(y+z−1)H)+NayKz(with possible loss of water or ammonia), where x, y, and z may vary from 0 to 8. In addition to these peaks, there is a background noise of complex structure that spans the entire range of mass-to-charge ratios, and which may mask peaks representing the analyte molecule(s) and its fragments. Chemical noise may be particularly problematic in high-throughput operations where careful and frequent cleaning of the MALDI substrate surface (which eliminates some sources of chemical noise) is not practical.
Because the chemical noise imposes a practical lower limit on sensitivity (the minimum analyte quantity that can be reliably detected by a mass spectrometer), there is a strong motivation to develop techniques that eliminate or minimize chemical noise sources. One such technique involves heating the matrix cluster ions to a temperature sufficient to break the relatively weak non-covalent bonds, such as hydrogen bonds or Van der Waals forces, which hold the matrix clusters together. However, applying heat thermally to the matrix cluster ions may have the undesirable effect of promoting decomposition of labile analyte ions. Furthermore, heating the analyte ions increases their kinetic energy and may adversely affect transmission and trapping efficiencies.